Package picard.fingerprint
Class HaplotypeProbabilitiesFromGenotype
- java.lang.Object
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- picard.fingerprint.HaplotypeProbabilities
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- picard.fingerprint.HaplotypeProbabilitiesFromGenotype
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public class HaplotypeProbabilitiesFromGenotype extends HaplotypeProbabilities
Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities
HaplotypeProbabilities.Genotype
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Constructor Summary
Constructors Constructor Description HaplotypeProbabilitiesFromGenotype(HaplotypeProbabilitiesFromGenotype other)
HaplotypeProbabilitiesFromGenotype(Snp snp, HaplotypeBlock haplotypeBlock, double AA, double Aa, double aa)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description HaplotypeProbabilitiesFromGenotype
deepCopy()
double[]
getLikelihoods()
Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidenceSnp
getRepresentativeSnp()
Returns the SNP who's genotype was used to construct the likelihoods.HaplotypeProbabilitiesFromGenotype
merge(HaplotypeProbabilities other)
Merges in the likelihood information from the supplied haplotype probabilities object.-
Methods inherited from class picard.fingerprint.HaplotypeProbabilities
getHaplotype, getLodMostProbableGenotype, getLogLikelihoods, getMostLikelyGenotype, getMostLikelyHaplotype, getObsAllele1, getObsAllele2, getPosteriorLikelihoods, getPosteriorProbabilities, getPriorProbablities, getTotalObs, hasEvidence, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies
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Constructor Detail
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HaplotypeProbabilitiesFromGenotype
public HaplotypeProbabilitiesFromGenotype(HaplotypeProbabilitiesFromGenotype other)
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HaplotypeProbabilitiesFromGenotype
public HaplotypeProbabilitiesFromGenotype(Snp snp, HaplotypeBlock haplotypeBlock, double AA, double Aa, double aa)
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Method Detail
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deepCopy
public HaplotypeProbabilitiesFromGenotype deepCopy()
- Specified by:
deepCopy
in classHaplotypeProbabilities
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getRepresentativeSnp
public Snp getRepresentativeSnp()
Returns the SNP who's genotype was used to construct the likelihoods.- Specified by:
getRepresentativeSnp
in classHaplotypeProbabilities
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getLikelihoods
public double[] getLikelihoods()
Description copied from class:HaplotypeProbabilities
Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidenceMathematically this is P(evidence | haplotype) where haplotype={AA,Aa,aa}. Will be normalized.
- Specified by:
getLikelihoods
in classHaplotypeProbabilities
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merge
public HaplotypeProbabilitiesFromGenotype merge(HaplotypeProbabilities other)
Description copied from class:HaplotypeProbabilities
Merges in the likelihood information from the supplied haplotype probabilities object.- Specified by:
merge
in classHaplotypeProbabilities
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